EP0173339B1 - Composé et méthode pour la détection de la présence d'une séquence déterminée d'un polynucléotide - Google Patents

Composé et méthode pour la détection de la présence d'une séquence déterminée d'un polynucléotide Download PDF

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Publication number
EP0173339B1
EP0173339B1 EP85110910A EP85110910A EP0173339B1 EP 0173339 B1 EP0173339 B1 EP 0173339B1 EP 85110910 A EP85110910 A EP 85110910A EP 85110910 A EP85110910 A EP 85110910A EP 0173339 B1 EP0173339 B1 EP 0173339B1
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Prior art keywords
polynucleotide sequence
interest
polynucleotide
composition
labeled
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German (de)
English (en)
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EP0173339A2 (fr
EP0173339A3 (en
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Elazar Rabbani
Dean L. Engelhardt
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Enzo Biochem Inc
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Enzo Biochem Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6832—Enhancement of hybridisation reaction
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Definitions

  • the present invention relates to a wide range of genetic analyses using the technique of nucleic acid hybridization. These genetic analyses include, for example, the diagnosis of infections by foreign microbes and the detection of specific genetic traits and abnormalities. More specifically, the present invention is related to the detection of the presence of a polynucleotide sequence of interest.
  • a general method for the detection of a polynucleotide sequence of interest in a sample comprises:
  • composition further comprises a second polynucleotide sequence which, either in the same molecule or a separate molecule, is not substantially complementary to said polynucleotide sequence of interest and which is labeled with said detectable marker; and (2) said polynucleotide sequence of interest is potentially contained in a sample that comprises polynucleotide sequences not of interest.
  • any signal detection is ambiguous as to whether said polynucleotide sequence of interest is detected or some polynucleotide sequences not of interest but hybridizable to said labeled second polynucleotide sequence are detected.
  • condition (1) presents itself quite naturally when said first polynucleotide sequence is produced by recombinant nucleic acid technology.
  • Recombinant nucleic acid technology allows economic large scale production of said first polynucleotide sequence concommitant with a second polynucleotide sequence which is not substantially complementary to the polynucleotide sequence of interest, the vector sequence in this instance, on the same molecule, i.e. the recombinant molecule.
  • this also produces a labeled second polynucleotide sequence, i.e. the vector sequence in this instance, which is not substantially complementary to said polynucleotide of interest.
  • condition (1) presents itself when said first polynucleotide sequence is inserted, along with a second polynucleotide sequence not substantially complementary to the polynucleotide sequence of interest, into a vector to form a single recombinant molecule. This is due to the fact that it is difficult or inconvenient to separate the first polynucleotide sequence from the second polynucleotide sequence or that the boundary between said first polynucleotide sequence and said second polynucleotide sequence is not known.
  • the labeled second polynucleotide sequence is capable of hybridizing to a complementary polynucleotide sequence that may be contained in the sample, i.e. condition (2) is present. This can generate a false positive result.
  • EP-A 0 076 123 discloses a method of characterizing an unknown organism which comprises comparing the chromatographic pattern of restriction endonuclease-digested DNA from said organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information-containing nucleic acid from or derived from a probe organism, with equivalent chromatographic patterns of at least two known different organism species.
  • the present invention provides a composition for detecting a polynucleotide sequence of interest in a sample which may contain polynucleotide sequences not of interest, which comprises:
  • the present invention further provides a method, for the detection of a polynucleotide sequence of interest in the potential or actual presence of polynucleotide sequences not of interest in a sample to be examined, which comprises:
  • the present invention is related to the detection of a polynucleotide sequence of interest.
  • the present invention is related to the detection of a polynucleotide sequence of interest in a diagnostic sample.
  • the polynucleotide sequence of interest can be any polynucleotide sequence present naturally in a sample or added to the sample. It can be in a material in or derived from a cellular system. It can be a subcellular component as virus or viroid or virus like particule. It can be a deoxyribonucleic acid sequence or a ribonucleic acid sequence. It can be single stranded or double stranded. It can be derived from a pathogen.
  • It can be a sequence of a prokaryote, such as Neisseria meningitidis or Neisseria gonorrhoea ; a eukaryote, such as human, or a virus such as herpes simplex virus I or herpes simplex virus II, or an extra chromosomal genetic element such as a B-lactamase specifying plasmid.
  • a prokaryote such as Neisseria meningitidis or Neisseria gonorrhoea
  • a eukaryote such as human
  • a virus such as herpes simplex virus I or herpes simplex virus II
  • an extra chromosomal genetic element such as a B-lactamase specifying plasmid.
  • the polynucleotide sequence of interest can be derived from all or any part of the genome.
  • the present invention is related to compositions of polynucleotide sequences that are useful in nucleic acid hybridizations.
  • the compositions comprise a first polynucleotide sequence which is substantially complementary to and capable of hybridizing to a specific polynucleotide sequence of interest and which is labeled with a first detectable marker; a second polynucleotide sequence that is not substantially complementary to or substantially identical to said polynucleotide sequence of interest and that is labeled with said first detectable marker; and a third polynucleotide sequence that is substantially complementary to or substantially identical to said second polynucleotide sequence and that is unlabeled or labeled with a second detectable marker.
  • the first and second polynucleotide sequences can be present as separate molecules or can be covalently linked.
  • the third polynucleotide sequence is present as a separate molecule.
  • the first, second and third polynucleotide sequences of the compositions of the present invention can be deoxyribonucleic acid or ribonucleic acid sequences and can be either single-stranded or double-stranded molecules.
  • the polynucleotide sequences can be produced or obtained by any method known to those of ordinary skill in the art, e.g., synthetic production methods or enzymatic production methods, both in vitro and in vivo .
  • the presence of the third polynucleotide sequence in the compositions of the invention serves to block the hybridization of the second polynucleotide sequence to any polynucleotide sequences not of interest in the sample being examined, which nevertheless are substantially complementary to said second polynucleotide sequence.
  • This blocking action limits the liklihood that the second polynucleotide sequence will generate a false positive result.
  • the first polynucleotide sequence that is substantially complementary to and capable of hybridizing to the polynucleotide sequence of interest, is cloned into a vector by standard recombinant nucleic acid technology to form a recombinant molecule.
  • the recombinant molecule comprises the first polynucleotide sequence and the second polynucleotide sequence, i.e. the vector in this embodiment of the invention.
  • the vector can be a plasmid, a cosmid, a bacterial virus or an animal virus.
  • the vector can be ribonucleic acid or deoxyribonucleic acid.
  • the vector can be single stranded or double stranded.
  • the first polynucleotide sequence which is part of the recombinant molecule, can be produced economically in large quantities inside hosts, for example, Escherichia coli by fermentation.
  • the recombinant molecule can be purified by standard methods.
  • the first polynucleotide sequence present in the recombinant molecule with a first detectable marker. This can be done in more than one way.
  • the first polynucleotide sequence is largely separated from the vector by, for example, cutting the recombinant molecule with a restriction enzyme followed by agarose gel electrophoresis, extracted and labeled. Thus, substantially only the first polynucleotide sequence and not the vector is labeled.
  • the entire recombinant molecule is labeled.
  • This method can be carried out by, for example, nick translation using DNAse I and DNA Polymerase I in the presence of labeled nucleoside triphosphates. (Rigby, P. W. et. al., J. Mol. Biol. 113:237 (1977)). This results in the recombinant molecule, i.e. the first and second polynucleotide sequences, being uniformly labeled.
  • the second method avoids numerous drawbacks incurred by the first method.
  • the first method is extremely tedious; each step is very time consuming, especially the step of gel electrophoresis. Often the step of gel electrophoresis needs to be repeated to insure purity of the separation of the first polynucleotide sequence. Even so, the first polynucleotide sequence may still be contaminated by trace amounts of the second polynucleotide sequence, i.e. the vector sequence. In such a case, the present invention provides a benefit.
  • the inherent properties of the recombinant molecules may be such that the first and second polynucleotide sequences can not be easily separated. For example, if the first polynucleotide sequence were of the same or similar size as the second polynucleotide sequence, then the separation of such two polynucleotide sequences may not be feasible.
  • the method of choice for labeling the first polynucleotide sequence causes the second polynucleotide sequence to be labeled also, and if polynucleotide sequences complementary to the second polynucleotide sequence are contained in the sample being examined, the interpretation of results of analysis based on the detection of labeled and hybridized polynucleotide sequences becomes problematic.
  • the second polynucleotide sequence is capable of generating a false positive result.
  • compositions of the invention comprise a third polynucleotide sequence.
  • the third polynucleotide sequence is either unlabeled or labeled with a second detectable marker and is substantially complementary to or substantially identical to the second polynucleotide sequence.
  • the presence of the third polynucleotide sequence in the compositions of the invention serves to block the hybridization of the second polynucleotide sequence to any polynucleotide sequences not of interest in the sample being examined, which nevertheless are substantially complementary to said second polynucleotide sequence. It is believed that this blocking action is achieved in either or both of two ways.
  • the third polynucleotide sequence being substantially complementary to said second polynucleotide sequence, can hybridize with the second polynucleotide sequence if said second and third polynucleotide sequences are rendered single stranded and allowed to contact under conditions that permit hybridization.
  • the third polynucleotide sequence being substantially identical to the second polynucleotide sequence, can hybridize to any polynucleotide sequences not of interest but complementary to the second polynucleotide sequence and present in the sample being examined. It is believed that either of these blocking actions inhibit the liklihood of the generation of a false positive result.
  • the first polynucleotide sequence which is substantially complementary to and capable of hybridizing to the polynucleotide sequence of interest, is covalently linked in the chromosome to the second polynucleotide sequence that is not substantially complementary or substantially identical to the polynucleotide sequence of interest, but which can potentially be substantially complementary to polynucleotide sequences not of interest in the sample being examined.
  • the first polynucleotide sequence and the second polynucleotide sequence can have a single boundary or multiple boundaries. The boundaries can be known or unknown. In some instances, it is difficult at best and generally impossible to isolate said first polynucleotide sequence from said second polynucleotide sequence. Consequently, it is preferable to label both the first and second polynucleotide sequences.
  • a specific example of this embodiment of the present invention is wherein the first polynucleotide sequence is a polynucleotide sequence specific for genetic material of Neisseria gonorrhoea .
  • a polynucleotide sequence is said to be specific for polynucleotide sequence A if and only if said polynucleotide sequence is capable of hybridizing exclusively to polynucleotide sequence A.
  • Neisseria gonorrhoea and Neisseria meningitidis share significant nucleic acid homology; in excess of 80% of the polynucleotide sequence of the Neisseria gonorrhoea genome is substantially complementary or substantially identical to the polynucleotide sequence of the Neisseria meningitidis genome (Kingsbury, D.T. J. Bact. (1967) 94, p 870-874).
  • a polynucleotide fragment, derived from Neisseria gonorrhoea deoxyribonucleic acid comprising a first polynucleotide sequence specific for N .
  • composition of the invention provides, in addition to such labeled first and second polynucleotide sequences, a third polynucleotide sequence which is not labeled with said first detectable marker and which is substantially complementary to or substantially identical to said second polynucleotide sequence.
  • the third polynucleotide sequence when present in suitable amounts, will effectively prevent said labeled second polynucleotide sequence from hybridizing to the polynucleotide sequence not of interest, i.e. the sample may comprise N . meningitidis DNA. Thus, a false positive signal will not be generated.
  • the third polynucleotide sequence can be provided in one of several ways.
  • a recombinant molecule consisting of a vector and an inserted polynucleotide sequence, isolated from N . meningitidis, which comprises a polynucleotide sequence or sequences which are substantially complementary or substantially identical to said second polynucleotide sequence can be added to the composition.
  • total genomic N . meningitidis DNA which comprises the third polynucleotide sequence, can be added to the composition.
  • the specific polynucleotide sequence of interest is a sequence specific for herpes simplex virus I.
  • the first polynucleotide sequence is specific for herpes simplex virus I DNA.
  • the second polynucleotide sequence which is labeled is a sequence specific for herpes simplex virus I DNA and herpes simplex virus II DNA.
  • the third polynucleotide sequence which is not labeled is a sequence substantially complementary to or substantially identical to said second polynucleotide sequence, i.e. that portion of herpes simplex virus II DNA that is specific for herpes simplex virus I DNA and herpes simplex virus II DNA, if known.
  • Said third polynucleotide sequence can be provided, for example, by including in the composition, total genomic herpes simplex virus II DNA.
  • This composition permits the detection of the specific polynucleotide sequence of interest, i.e. herpes simplex virus I DNA and inhibits the liklihood of the second polynucleotide sequence from detecting herpes simplex virus II DNA.
  • the first polynucleotide sequence i.e. the polynucleotide sequence that is substantially complementary to and capable of hybridizing to the polynucleotide sequence of interest, is produced inside hosts as an extrachromosomal polynucleotide sequence.
  • the second polynucleotide sequence is the host polynucleotide sequence.
  • the first polynucleotide sequence can be substantially purified by standard methods. However, it may be contaminated with a trace amount of the second polynucleotide sequence, i.e. the host polynucleotide sequence. Thus, when the first polynucleotide sequence is labeled with a first detectable marker, a trace amount of the host polynucleotide sequence is also labeled. If the sample to be examined contains polynucleotide sequences complementary to the second polynucleotide sequence, i.e. the host polynucleotide sequence, a false positive result can be generated. To prevent this undersirable result, the composition of the invention provides a third polynucleotide sequence which, in this embodiment, is the host sequence that is not labeled with said first detectable marker.
  • a specific example of this embodiment of the present invention is wherein the first polynucleotide sequence is an enteroinvasive plasmid, which is grown in E . coli hosts.
  • the sample to be examined is derived from the stool of a human patient. This sample is then expected to contain E . coli polynucleotide sequence. If the labeled first polynucleotide sequence is contaminated even with a small amount of labeled second polynucleotide sequence, i.e. E . coli polynucleotide sequence, a false positive result can be generated. However, inclusion of a third polynucleotide sequence, i.e. unlabeled E . coli polynucleotide sequence, will inhibit the likelihood of this undesirable result.
  • the three embodiments discussed above namely, the second polynucleotide sequence as a vector sequence, the second polynucleotide sequence as a sequence chromosomally linked to the first polynucleotide sequence and the second polynucleotide sequence as a host polynucleotide sequence can be combined.
  • the third polynucleotide sequence which is not labeled with the first detectable marker, can comprise a sequence which is substantially complementary or substantially identical to said vector sequence and said sequence which is chromosomally linked to said first polynucleotide sequence, and a polynucleotide host sequence.
  • the third polynucleotide sequence fragments can be essentially any length, provided that the fragments are long enough to form a stable hybrid.
  • a preferred embodiment of the invention is wherein the third polynucleotide sequence fragments are from about 50 to about 250 nucleotides in length. These short fragments are preferably produced by controlled digestion with DNAse I. Alternatively, sonication or digestion with other suitable nucleases can be used.
  • a labeled polynucleotide sequence in this invention means a polynucleotide sequence which is labeled with a detectable marker.
  • Any detectable markers now in use in the art of nucleic acid hybridization or to be developed in the future can be used.
  • the choice of detectable markers, is not critical to the present invention. Suitable detectable markers include radioactive nuclides; chemical markers including biotinated moieties, antigens, sugars, fluors and phosphors, enzymes, apoenzymes and cofactors, ligands, allosteric effectors, ferritin, dyes, microspheres.
  • a first detectable marker is said to differ from a second detectable marker in the context of the present invention whenever an effective method exists and is used, that discriminates said first detectable marker from said second detectable marker.
  • 3H and 32P are both radioactive markers. They are different detectable markers in the context of programmed scintillation counting that discriminate higher energy disintegrations of 32P from low energy disintegration from 3H. They are not different detectable markers if the scintillation counting does not discriminate the energy of disintegration.
  • A is a polynucleotide sequence labeled with biotinylated nucleotides
  • B is a polynucleotide sequence labeled at the 3'terminus with poly T.
  • A is detected by an avidin-horseradish peroxidase complex which generates a color in the presence of a suitable chromogen substrate.
  • the present invention also relates to methods of using the compositions of the present invention.
  • the compositions can be used in all nucleic acid hybridization procedures. These procedures include, but are not limited to two phase hybridization and one phase hybridization. Examples of two phase hybridization are hybridization in situ and hybridization to polynucleotide sequences immobilized on a transparent and nontransparent surface. An example of one phase hybridization is hybridization to polynucleotide sequences in solution. The choice of a particular procedure is not critical to the present invention.
  • the genetic material of the sample to be examined is prepared as called for in the particular procedure being used, which is or will be known to a person of ordinary skill in the art. These procedures result in at least a portion of the genetic material of the sample being in single stranded form, but preferably substantially all of the genetic material of the sample is in single stranded form.
  • polynucleotide sequences of the compositions of the invention are rendered in single stranded form.
  • said polynucleotide sequences be rendered in substantially single stranded form because polynucleotide sequences in duplex form generally do not participate in hybridization.
  • Each component, namely, the first polynucleotide sequence, the second polynucleotide sequence and the third polynucleotide sequence can be rendered in substantially single stranded form singly or together in any combination.
  • the polynucleotide sequences in said composition are utilized to contact the prepared genetic material of the sample to be examined, which has been rendered in single stranded form, under conditions that permit hybridization. It is highly preferred that the third polynucleotide sequence be allowed to contact the prepared sample prior to, or at substantially the same time as the second polynucleotide sequence. Otherwise, given time during which the third polynucleotide sequence is absent, the second polynucleotide sequence can hybridize to complementary polynucleotide sequences not of interest, if present, in the sample being examined. This would defeat the purpose of including the third polynucleotide sequence in the composition and generate a false positive result upon detection of the first detectable marker. Within this preferred condition, there are three preferred embodiments for practicing the method of the invention.
  • the first, second and third polynucleotide sequences of the composition are contacted with the sample to be examined at about the same time.
  • the third polynucleotide sequence is present in the composition in an amount by weight from about 100 to about 1000 fold greater than the amount of the second polynucleotide sequence in the composition. Amounts greater than about 1000 fold blocked essentially no more of the second polynucleotide sequence.
  • the third polynucleotide sequence should be present in an amount by weight from about 100 to about 1000 fold greater than the amount of the polynucleotide sequence not of interest but capable of hybridizing to the second polynucleotide sequence.
  • the latter situation is very rarely of concern.
  • the first, second and third polynucleotide sequences are allowed to contact each other in solution and hybridize for a substantial amount of time so that the hybridization of the second polynucleotide sequence is substantially complete and that the hybridization of the first polynucleotide sequence is not.
  • the third polynucleotide sequence be present in the composition in an amount by weight from about 100 to about 1000 fold greater than the amount of the second polynucleotide sequence in the composition. This excess of the third polynucleotide sequence accelerates the hybridization of the second polynucleotide sequence without accelerating the renaturation of the first polynucleotide sequence.
  • this embodiment is less preferred. But this embodiment of the invention is more preferred if the sample to be examined contains sigificant amounts of polynucleotide sequences not of interest but capable of hybridizing to the second polynucleotide sequence. This is because the second polynucleotide sequence in the composition has already hybridized substantially to completion and can not hybridize to any polynucleotide sequence in the sample.
  • the third polynucleotide sequence of the composition is allowed to contact with and hybridize substantially to completion with the genetic material in the sample to be examined prior to the contacting of the second polynucleotide sequence with the genetic material in the sample.
  • the third polynucleotide sequence be present in the composition in an amount by weight from about 10 fold to about 100 fold greater than the amount of the polynucleotide sequence not of interest but capable of hybridizing to the second polynucleotide sequence in the composition. This amount is generally sufficient to hybridize with all polynucleotide sequences not of interest but capable of hybridizing to the second polynucleotide sequence in the composition.
  • This embodiment is not preferred with respect to the extra time required and the extra step necessary to obtain a result. But it is preferred with respect to the quantity of the third polynucleotide sequence required for the composition when the sample to be examined contains significant amounts of polynucleotide sequence not of interest but capable of hybridizing to the second polynucleotide sequence.
  • the stable hybrid genetic material formed is detected by means of the first detectable marker.
  • the detection step requires a separation step which separates that part of the composition which has hybridized to the sample being examined from that part which has not.
  • separation can be carried out by a wash step.
  • the sample to be examined is immobilized on a nitrocellulose filter. Biotinylated nucleotides are used to label the first and second polynucleotide sequences.
  • the nitrocellulose filter is washed so that unhybridized sequences in the composition are removed.
  • the biotinylated nucleotides contained in the molecules which are bound to the immobilized target are then detected by any suitable means.
  • a separation step is not necessary in the detection process.
  • the detectable marker used is an asymmetric chemiluminescent emitter/absorber system.
  • a signal is generated only if the labeled polynucleotide sequences in the composition have hybridized with substantially complementary sequences in the sample being examined.
  • This method of detection is disclosed in European Patent Publication 0 070 685, published January 26. 1983.
  • Another example utilizes agglutinable microsphere as the detectable marker. This method is disclosed in co-pending, co-assigned U.S. Patent Application Serial No.
  • the third polynucleotide sequence of the composition can, if so desired, be labeled with a second detectable marker. It is then possible to detect any third polynucleotide sequence that hybridizes with the genetic material in the sample, and, by inference, the presence of a polynucleotide sequence not of interest but capable of hybridizing to the second polynucleotide sequence of the composition. Such detection can give a benefit if the quantity of said polynucleotide sequence not of interest in the sample is large, as indicated by the signal generated by the second detectable marker, it may become necessary to re-assess the significance of a positive result, if any, from the first detectable marker. This is because some fraction of the second polynucleotide sequence may have hybridized to said polynucleotide sequence not of interest in the sample and contributed to the signal from the first detectable marker.
  • a model system was used to demonstrate the detection of a polynucleotide sequence of interest, a 9 kilobase DNA fragment of Chlamydia trachomatis , in the presence of a polynucleotide not of interest, pBR322.
  • the plasmid pCHL2 consists of a 9 kilobase BamH I fragment from Chlamydia trachomatis cloned into the BamH I site of the plasmid pBR322.
  • the 9 kilobase BamH I fragment has no substantial complementarity to pBR322.
  • Sonicated pCHL2 plasmid DNA at a concentration of 220ug/ml in 10mM Tris-HCl pH 7.5, 0.1mM EDTA was denatured by the addition of NaOH to a final concentration of 0.5M.
  • a volume of 1M Tris-HCl pH 7.5 equal to that of the alkaline DNA solution was added to neutralize the solution.
  • An amount equivalent to 2 ⁇ g of DNA was then applied to each of 30 points on a nitrocellulose filter (previously wetted with distilled water at 65°C.
  • pCHL2 was digested with the restriction enzyme BamH I, and the resulting fragments separated on an 0.5% low melting temperature agarose gel. The band corresponding in size to 9.0 kb was cut from the gel, and the DNA extracted from the gel slice using sodium iodide and powdered flint glass as described by Vogelstein and Gillespie (Proc. Natl. Acad. Sci. USA 76 : 615-617, 1979). An aliquot of this purified fragment was run on 0.7% agarose gel to check for contamination of the purified chlamydia fragment by the pBR322 vector. No contamination of the pure fragment was seen. However, the remaining chlamydia DNA fragment was subjected to a second round of gel electrophoresis and isolation to obviate any possibility of contamination by the pBR322 vector sequence.
  • Pure chlamydia fragment DNA was nick translated with 32P labeled nucleotides to a specific activity of 2.1 x 107 cpm/ ⁇ g and pBR322 was nick translated with 3H labeled nucleotides to a specific activity of 3 x 106 cpm/ ⁇ g.
  • Hybridizations were carried out in 1.5 ml Eppendorf tubes in a total volume of 500 ⁇ l and contained 3X SSC, 5X Denhardt's, 0.1% SDS and 100 ⁇ g/ml calf thymus DNA.
  • Tubes 1 to 16 received a nitrocellulose filter disc with pCHL2 DNA.
  • Tubes 17 to 32 received control discs with no target sequence.
  • Unlabeled, DNase I digested pBR322 DNA was boiled for 5 to 7 minutes and then placed on ice. It was added to tubes 1 to 16 and 17 to 32 in amounts by weight representing 0, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 500 and 1000 fold excess over the amount of 3H labeled pBR322 DNA.
  • a second channel was set to detect high energy 32P disintegrations in the range of 500 to 1000. Under these conditions, spill-over into the first channel by 32P counts was 1.65% that of the second channel counts and spillover into the second channel by 3H counts was less than 0.1% that of the first channel.
  • any amount of unlabeled pBR322 that has been digested by DNase I to a size varying from about 25 to about 125 nucleotides in length was more effective than the same amount of unlabeled, full length linear pBR322 in blocking the hybridization of labeled pBR322 DNA to its complementary sequence target.
  • Example I The same plasmids cited in Example I, namely, pCHL2, pBR322 were used.
  • the 9 kilobase DNA fragment from Chlamydia trachomatis was purified as described in Example I. Intact, supercoiled pBR322 DNA was disrupted by brief sonication. Separately, each DNA was treated sequentially with NaOH, Tris-HCl pH 7.5 and 20X SSC as described in Example I. 200 ng samples of pBR322 DNA or Chlamydia trachomatis DNA were applied on nitrocellulose filters as described in Example I. The filters were then dried and baked for 2 hours at 80 o C in vacuo . Each spot on the filter was then cut out to yield 3/16 inch diameter circular filters containing Chlamydia trachomatis DNA or 3/16 inch x 3/16 inch square filters containing pBR322 DNA or control filters of 3/16 inch diameter containing no DNA.
  • unlabeled, DNased pBR322 DNA or BamH I digested pBR322 DNA was added in varying amounts and corresponding to a 0, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 500 or 1000 fold excess by weight over the labeled probe.
  • 26 control hybridizations were set up in the same way except that one nitrocellulose filter which contained no target DNA sequence was added to each hybridization. Hybridization and washing conditions were as previously described in Example I.
  • This example illustrates how a recombinant plasmid, consisting of a DNA fragment from Neisseria gonorrhea cloned into the vector pBR322, can be used to detect N .
  • gonorrhea DNA even if said fragment comprises a sequence that is a substantially complementary to some sequence of Neisseria meningitidis .
  • pAL1 consists of a 1.1kb fragment of N . gonorrhea DNA cloned into the Pst I site of pBR322 by the homopolymer dG:dC tailing method.
  • N . gonorrhea or N . meningitidis Chromosomal DNA from N . gonorrhea or N . meningitidis was prepared by the method of Marmur (J. Mol. Biol. 3: 208-218, (1961). 2 ⁇ g of N . gonorrhea DNA or 2 ⁇ g of N . meningitidis DNA were immobilized on each of 16 circular and square nitrocellulose filters respectively as described in Examples I and II. Control filters contain no DNA.
  • Plasmid pAL1 DNA was labeled by nick translation as described previously in Example I using four 32P labeled nucleotides. The specific activity of the labeled DNA was 2.7 x 108 cpm/ ⁇ g. 1.25 x 105 cpm of the radioactively labeled probe were to be added to each 500ul hybridization reaction, corresponding to 0.47 ⁇ g of probe DNA.
  • Hybridizations were set up at 65 o C and contained 3X SSC, 5X Denhardt's, 0.1% SDS and 100ug/ml calf thymus DNA. Tubes 1 to 16 received one circular filter with 2 ⁇ g of N . gonorrhoeae DNA and one square filter with 2 ⁇ g of N . meningitidis DNA. Tubes 17 and 32 received one control filter. Unlabeled pBR322 DNA was added at 1000 fold excess and unlabeled N .
  • meningitidis DNA was added at a 0, 125, 250, 500, 103, 2 x 103, 3.9 x 103, 7.8 x 103, 1.6 x 104, 6.25 x 104, 1.25 x 105, 2.5 x 105, 5 x 105 106 and 2 x 106 fold excess over the amount of pAL1 probe DNA.
  • DNA was boiled for 5 to 7 minutes and then placed on ice before addition to hybridization reactions. Hybridization was carried out for 16 hours at 65 o C.
  • the filters were then rinsed 3 times with 2 X SSC, 0.1% SDS at 65 o C. Filters were dried under an infrared lamp and counted separately in a Beckman LS6800 scintillation counts using a standard scintillation cocktail.

Claims (16)

  1. Composition pour détecter une séquence polynucléotidique intéressante dans un échantillon qui peut contenir des séquences polynucléotidiques non intéressantes, comprenant:
    (a) une première séquence polynucléotidique où ladite première séquence polynucléotidique est sensiblement complémentaire de et capable de s'hybrider à ladite séquence polynucléotidique intéressante et est marquée avec un premier marqueur détectable;
    (b) une seconde séquence polynucléotidique où ladite seconde séquence polynucléotidique n'est pas sensiblement complémentaire de ou sensiblement identique à ladite séquence polynucléotidique intéressante et est marquée avec ledit premier marqueur détectable; et
    (c) une troisième séquence polynucléotidique où ladite troisième séquence polynucléotidique est sensiblement complémentaire de ou identique à ladite seconde séquence polynucléotidique et est soit non marquée, soit marquée avec un second marqueur détectable.
  2. Composition selon la revendication 1, dans laquelle ladite première séquence polynucléotidique et ladite seconde séquence polynucléotidique sont dérivées d'une molécule recombinante où ladite seconde séquence polynucléotidique comprend une séquence polynucléotidique vectrice.
  3. Composition selon la revendication 1, dans laquelle ladite première séquence polynucléotidique est liée de façon covalente à ladite seconde séquence polynucléctidique dans un chromosome.
  4. Composition selon la revendication 3 dans laquelle ladite première séquence polynucléotidique est spécifique d'une séquence polynucléotidique choisie parmi N. gonorrhoea, le virus I d'Herpes simplex, le virus II d'Herpes simplex, Brucella abortus, Bordetella pertussis, Shigella dysenteria, Haemophilus influenzae, Mycobacterium tuberculosis, Pseudomonas pseudomallei, Salmonella typhi, Salmonella typhimurium ou N. meningitidis.
  5. Composition selon la revendication 1, dans laquelle ladite séquence polynucléotidique est une séquence polynucléotidique hôte.
  6. Composition selon la revendication 1, dans laquelle ladite troisième séquence polynucléotidique est non marquée.
  7. Procédé de détection d'une séquence polynucléotidique intéressante dans la présence potentielle ou effective de séquences polynucléotidiques non intéressantes, dans laquelle:
    (A) on fournit une composition qui comprend:
    (i) une première séquence polynucléotidique dans laquelle ladite première séquence polynucléotidique est sensiblement complémentaire de et capable de s'hybrider à ladite séquence polynucléotidique intéressante et est marquée avec un premier marqueur détectable;
    (ii) une seconde séquence polynucléotidique dans laquelle ladite seconde séquence polynucléotidique n'est pas sensiblement complémentaire de ou sensiblement identique à ladite séquence polynucléotidique intéressante et est marquée avec ledit premier marqueur détectable;
    (iii) une troisième séquence polynucléotidique où ladite troisième séquence polynucléotidique est sensiblement complémentaire de ou identique à ladite seconde séquence polynucléotidique et est soit non marquée, soit marquée avec un second marqueur détectable;
    (B) on met au moins une partie de ladite séquence polynucléotidique intéressante et desdites séquences polynucléotidiques non intéressantes sous une forme à un seul brin;
    (C) on met au moins une partie de ladite composition sous une forme à un seul brin;
    (D) on met en contact ladite séquence polynucléotidique intéressante et lesdites séquences polynucléotidiques non intéressantes dans ledit échantillon avec ladite composition dans des conditions permettant l'hybridation;
    et
    (E) on détecte ladite séquence polynucléotidique intéressante au moyen dudit premier marqueur détectable.
  8. Procédé selon la revendication 7, dans lequel la presque totalité de ladite séquence polynucléotidique intéressante et desdites séquences polynucléotidiques non intéressantes sont mises sous une forme à un seul brin et la presque totalité de ladite composition est mise sous une forme à un seul brin.
  9. Procédé selon la revendication 8, dans lequel ladite séquence polynucléotidique intéressante et lesdites séquences polynucléotidiques non intéressantes sont mises en contact avec ladite troisième séquence polynucléotidique avant la mise en contact de la séquence nucléotidique intéressante et des séquences polynucléotidiques non intéressantes dans ledit échantillon avec ladite première séquence polynucléotidique et ladite seconde séquence polynucléotidique.
  10. Procédé selon la revendication 8, dans lequel en outre on met en contact ladite seconde séquence polynucléotidique avec ladite troisième séquence polynucléotidique dans des conditions permettant l'hybridation après que ladite composition soit mise pratiquement sous une forme à un seul brin, mais avant que ladite séquence polynucléotidique intéressante et lesdites séquences polynucléotidiques non intéressantes soient mises en contact avec ladite composition.
  11. Composition en deux parties pour détecter une séquence polynucléotidique intéressante dans un échantillon qui peut contenir des séquences polynucléotidiques non intéressantes, une première partie de ladite composition comprenant:
    (a) une première séquence polynucléotidique où ladite première séquence polynucléotidique est sensiblement complémentaire de et capable de s'hybrider à ladite séquence polynucléotidique intéressante et est marquée avec un premier marqueur détectable; et
    (b) une seconde séquence polynucléotidique où ladite seconde séquence polynucléotidique n'est pas sensiblement complémentaire de ou sensiblement identique à ladite séquence polynucléotidique intéressante et est marquée avec ledit premier marqueur détectable;
    et une seconde partie de ladite composition comprenant:
    (c) une troisième séquence polynucléotidique où ladite troisième séquence polynucléotidique est sensiblement complémentaire de ou identique à ladite seconde séquence polynucléotidique et est soit non marquée, soit marquée avec un second marqueur détectable.
  12. Composition selon la revendication 11, dans laquelle ladite première séquence polynucléotidique et ladite seconde séquence polynucléotidique sont dérivées d'une molécule recombinante où ladite seconde séquence polynucléotidique comprend une séquence polynucléotidique vectrice.
  13. Composition selon la revendication 11 dans laquelle ladite première séquence polynucléotidique est liée de façon covalente à ladite seconde séquence polynucléotidique dans un chromosome.
  14. Composition selon la revendication 13 dans laquelle ladite première séquence polynucléotidique est spécifique d'une séquence polynucléotidique choisie parmi N. gonorrhoea, le virus I d'Herpes simplex, le virus II d'Herpes simplex, Brucella abortus, Bordetella pertussis, Mycobacterium tuberculosis, Pseudomonas pseudomallei, Salmonella typhi, Salmonella typhimurium ou N. meningitidis.
  15. Composition selon la revendication 11 dans laquelle ladite séquence polynucléotidique est une séquence polynucléotidique hôte.
  16. Composition selon la revendication 11 dans laquelle ladite troisième séquence polynucléotidique est non marquée.
EP85110910A 1984-08-30 1985-08-29 Composé et méthode pour la détection de la présence d'une séquence déterminée d'un polynucléotide Expired - Lifetime EP0173339B1 (fr)

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ES546536A0 (es) 1987-03-01
CA1260368A (fr) 1989-09-26
DK391985D0 (da) 1985-08-29
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US4755458A (en) 1988-07-05
ES8703934A1 (es) 1987-03-01
JPH0634758B2 (ja) 1994-05-11
ATE71982T1 (de) 1992-02-15
EP0173339A2 (fr) 1986-03-05
IL76143A (en) 1990-02-09
DK391985A (da) 1986-03-01
JPS6165163A (ja) 1986-04-03
NO853408L (no) 1986-03-03
AU4646685A (en) 1986-03-06
EP0173339A3 (en) 1987-12-23
IL76143A0 (en) 1985-12-31

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